void agpToFaOne(struct agpFrag **pAgpList, char *agpFile, char *agpSeq,
char *seqDir, int lastPos, FILE *f)
/* Given one sequence's worth of AGP in pAgpList, process it into FASTA
* and write to f. */
{
DNA *dna = NULL;
slReverse(pAgpList);
if (lastPos == 0)
errAbort("%s not found in %s\n", agpSeq, agpFile);
dna = needHugeMem(lastPos+1);
memset(dna, 'n', lastPos);
dna[lastPos] = 0;
if (optionExists("simpleMulti"))
{
simpleMultiFillInSequence(0, seqDir, *pAgpList, dna, lastPos);
}
else if (optionExists("simpleMultiMixed"))
{
simpleMultiFillInSequence(1, seqDir, *pAgpList, dna, lastPos);
}
else if (optionExists("simple"))
{
simpleFillInSequence(seqDir, *pAgpList, dna, lastPos);
}
else
{
gsFillInSequence(seqDir, *pAgpList, dna, lastPos);
}
verbose(2,"Writing %s (%d bases)\n", agpSeq, lastPos);
faWriteNext(f, agpSeq, dna, lastPos);
agpFragFreeList(pAgpList);
}
static void goldFree(struct track *tg)
/* Free up goldTrackGroup items. */
{
agpFragFreeList((struct agpFrag**)&tg->items);
agpGapFreeList((struct agpGap**)&tg->customPt);
}
void bedDown(char *database, char *table, char *faName, char *tabName)
/* bedDown - Make stuff to find a BED format submission in a new version. */
{
char query[512];
struct sqlConnection *conn = sqlConnect(database);
struct sqlConnection *conn2 = sqlConnect(database);
struct sqlResult *sr;
char **row;
struct bed bed;
static char nibChrom[64];
int nibStart = 0;
int nibSize = 0;
int nibEnd = 0;
int nibTargetSize = 512*1024;
struct dnaSeq *nibSeq = NULL;
int midPos;
int chromSize;
int s, e, sz;
FILE *fa = mustOpen(faName, "w");
FILE *tab = mustOpen(tabName, "w");
FILE *nib = NULL;
char nibFileName[512];
char seqName[512];
struct agpFrag *chromFragList = NULL, *frag, *fragsLeft = NULL;
int fragPos;
char *destName;
char *destStrand;
sqlSafef(query, sizeof query, "select chrom,chromStart,chromEnd,name from %s order by chrom,chromStart", table);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
bedStaticLoad(row, &bed);
/* Fix badly cased Exofish chromosomes mostly... */
if (sameString(bed.chrom, "chrna_random"))
bed.chrom = "chrNA_random";
else if (sameString(bed.chrom, "chrul_random"))
bed.chrom = "chrUL_random";
else if (sameString(bed.chrom, "chrx_random"))
bed.chrom = "chrX_random";
else if (sameString(bed.chrom, "chry_random"))
bed.chrom = "chrY_random";
else if (sameString(bed.chrom, "chrx"))
bed.chrom = "chrX";
else if (sameString(bed.chrom, "chry"))
bed.chrom = "chrY";
if (!sameString(bed.chrom, nibChrom))
{
strcpy(nibChrom, bed.chrom);
nibSize = nibStart = nibEnd = 0;
sqlSafef(query, sizeof query, "select fileName from chromInfo where chrom = '%s'", bed.chrom);
sqlQuickQuery(conn2, query, nibFileName, sizeof(nibFileName));
carefulClose(&nib);
nibOpenVerify(nibFileName, &nib, &chromSize);
agpFragFreeList(&chromFragList);
chromFragList = fragsLeft = loadChromAgp(conn2, bed.chrom);
printf("%s has %d bases in %d fragments\n", nibFileName, chromSize, slCount(chromFragList));
}
midPos = (bed.chromStart + bed.chromEnd)/2;
s = midPos - 200;
if (s < 0) s = 0;
e = midPos + 200;
if (e > chromSize) e = chromSize;
sz = e-s;
if (rangeIntersection(s,e,nibStart,nibEnd) < sz)
{
freeDnaSeq(&nibSeq);
nibStart = s;
nibSize = nibTargetSize;
if (nibSize < sz)
nibSize = sz;
nibEnd = nibStart + nibSize;
if (nibEnd > chromSize)
{
nibEnd = chromSize;
nibSize = nibEnd - nibStart;
}
nibSeq = nibLdPart(nibFileName, nib, chromSize, nibStart, nibSize);
}
if (findCoveringFrag(midPos, &fragsLeft, &frag, &fragPos))
{
destName = frag->frag;
destStrand = frag->strand;
}
else
{
destName = "?";
fragPos = 0;
destStrand = "+";
warn("Couldn't find %s@%s:%d in agpFrag list", bed.name, bed.chrom, midPos);
}
fprintf(tab, "%s\t%s\t%s\t%d\t%d\t%d\t%d\t%s\t%s\t%d\n",
bed.name, database, bed.chrom, bed.chromStart,
bed.chromEnd - bed.chromStart, s - bed.chromStart, e-bed.chromStart,
destName, destStrand, fragPos);
sprintf(seqName, "%s.%s.%s.%d", bed.name, database, bed.chrom,
bed.chromStart);
faWriteNext(fa, seqName, nibSeq->dna + s - nibStart, sz);
}
freeDnaSeq(&nibSeq);
sqlFreeResult(&sr);
sqlDisconnect(&conn);
sqlDisconnect(&conn2);
}
